Identification of molecular sequence signatures and methods involving the same

• US 7,135,285 B2
• Filed: 03/14/2002
• Issued: 11/14/2006
• Est. Priority Date: 09/19/1996
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lockhart, David J., Wong, Gordon G., Langer-Safer, Pennina
• Primary Examiner(s): Whisenant, Ethan
• Application Number:
  US10/099,442
• Publication Number:
  US 20030129604A1
• Time in Patent Office: 1,706 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 536/23.1, 536/24.3
• US Class Current: 435/6.13
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2565/515 characterised by the interaction between or sequential use of two or more arrays
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature, whether the target encodes a member of a gene family, or whether the target is derived from one of any number of genes.

Claims

1. A method for determining whether a DNA sample contains a gene family member, said method comprising

providing a polynucleotide array comprising a polynucleotide probe that defines a reference nucleotide sequence from the gene family member wherein the reference nucleotide sequence codes for an amino acid sequence and the array further comprises a probe set defining a degenerate set of nucleotide sequences encoding said amino acid sequence;

wherein the nucleotide sequences encoding said amino acid sequence are between 15 and 30 nucleotides in length, and

wherein the probe set defining said degenerate set comprises at least 25% of the nucleotide sequences encoding said degenerate set;

hybridizing said DNA sample to said probe array;

detecting the presence or absence of a sequence in said DNA sample hybridizing to said probe set defining said degenerate set of nucleotide sequences; and

determining whether the DNA in the sample contains a member of the gene family from the presence or absence of a sequence hybridizing to said probe set defining said degenerate set of nucleotide sequences.

2. The method of claim 1, wherein the probe set defining said degenerate set comprises at least 50% of the nucleotide sequences encoding said degenerate set.

3. The method of claim 1, wherein the probe set defining said degenerate set comprises at least 75% of the nucleotide sequences encoding said degenerate set.

4. The method of claim 1, wherein the probe set defining said degenerate set comprises at least 95% of the nucleotide sequences encoding said degenerate set.

5. The method of claim 1, wherein the probe set defining said degenerate set comprises the set of all nucleotide sequences encoding said degenerate set.